To ensure the safe transportation and efficient utilisation of lignite, it is important to inhibit its spontaneous combustion. In this study, Shengli lignite (SL⁺) was used as the research object and ionic liquids (ILs) were used to pretreat the lignite to investigate their effect on the combustion performance of lignite. On this basis, the relationship between the structure and combustion performance of lignite with different structures (heat treatment, oxidation) after ILs treatment was investigated. Results indicated that the combustion of lignite treated with ILs shifted towards higher temperatures. The most pronounced effect was observed in coal samples treated with [BMIM]Cl (1-butyl-3-methylimidazolium chloride), with the maximum combustion rate corresponding to a temperature increase of approximately 57 °C compared to that of the untreated lignite. For the heat-treated lignite, the temperature corresponding to the maximum combustion rate was approximately 38 °C higher than that of the untreated lignite. After [BMIM]Cl treatment, the combustion performance of the heat-treated lignite changed very slightly. In contrast, for oxidised lignite, the temperature corresponding to the maximum combustion rate decreased by approximately 54 °C compared with that of the untreated lignite and increased by approximately 135 °C after treatment with [BMIM]Cl. The characterisation results show that the content of aliphatic hydrogen and oxygen-containing functional groups decreased in the heat-treated lignite, while the content of hydroxyl and carboxyl groups increased in the oxidised lignite. The microstructure of the heat-treated lignite after [BMIM]Cl treatment changed slightly. In contrast, in the oxidised lignite after [BMIM]Cl treatment, the content of hydroxyl and carboxyl groups decreased, whereas the content of ether (C–O–) structures increased. The increased content of ether (C–O–) structures improved the stability of the coal samples. It is believed that the inhibition of lignite combustion is mainly attributed to the high stability of the ether (C–O–) structures. The kinetic analysis demonstrated that the ILs treatment increased the activation energy of lignite combustion.